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. Author manuscript; available in PMC: 2015 May 28.
Published in final edited form as: Proteins. 2008 Dec;73(4):1021–1036. doi: 10.1002/prot.22134

Figure 1.

Figure 1

Overall EC structure. (A) A snapshot from an umbrella sampling trajectory of the posttranslocated open complex. N-terminal, fingers, thumb, and palm domains are shown in silver, blue, green, and red, respectively. The template, nontemplate, and RNA strands are shown in orange, yellow, and dark green. (B) A snapshot [from Sampling 2 (Table II)] near the pretranslocated state of the open complex. The protein backbone is shown colored according to RMSD (blue: low, red: high) of each residue with respect to (A). The thumb helix break can be seen in comparison with (A) (Table I). (C) A snapshot from the unconstrained simulation of the pretranslocated closed complex. [Color figure can be viewed in the online issue, which is available at www.interscience.wiley.com.]